A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding

The hydroxyl radical footprint of the TATA-binding protein (TBP) bound to t he high-affinity sequence TATAAAAG of the adenovirus 2 major late promoter has been quantitatively compared to a 2 ns molecular dynamics simulation of the complex in aqueous solution at room temperature using the CHARMM23 pot ential. The nucleotide-by-nucleotide analysis of the TBP-TATA hydroxyl radi cal footprint correlates with the solvent-accessible surface calculated fro m the dynamics simulation. The results suggest that local reactivity toward s OH radicals results from the interplay between the local DNA geometry imp osed by TBP binding, and the dynamics of the side-chains contacting the sug ar hydrogen atoms. Analysis of the dynamics suggests that, over time, TBP f orms stable interactions with the sugar-phosphate backbone through multiple contacts to different partners. This mechanism results in an enthalpic adv antage to complex formation at a low entropic cost. (C) 2000 Academic Press .